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Exploration and analysis of DNA microarray and other high dimensional data / / Dhammika Amaratunga, Javier Cabrera, Ziv Shkedy, authors
| Exploration and analysis of DNA microarray and other high dimensional data / / Dhammika Amaratunga, Javier Cabrera, Ziv Shkedy, authors |
| Autore | Amaratunga Dhammika <1956-> |
| Edizione | [Second edition.] |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, , 2014 |
| Descrizione fisica | 1 online resource (346 p.) |
| Disciplina | 572/.636 |
| Altri autori (Persone) |
CabreraJavier
ShkedyZiv |
| Collana | Wiley series in probability and statistics |
| Soggetto topico | Protein microarrays - Statistical methods |
| ISBN |
1-118-36450-3
1-118-36453-8 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Contents; Preface; Chapter 1 A Brief Introduction; 1.1 A Note on Exploratory Data Analysis; 1.2 Computing Considerations and Software; 1.3 A Brief Outline of the Book; 1.4 Data Sets and Case Studies; 1.4.1 The Golub Data; 1.4.2 The Mouse5 Data; 1.4.3 The Khan Data; 1.4.4 The Sialin Data; 1.4.5 The Behavioral Study Data; 1.4.6 The Spiked-In Data; 1.4.7 The APOAI Study; 1.4.8 The Breast Cancer Data; 1.4.9 Platinum Spike Data Set; 1.4.10 Human Epidermal Squamous Carcinoma Cell Line A431 Experiment; 1.4.11 Note: Public Repositories of Microarray Data; Chapter 2 Genomics Basics
2.1 Genes2.2 Deoxyribonucleic Acid; 2.3 Gene Expression; 2.4 Hybridization Assays and Other Laboratory Techniques; 2.5 The Human Genome; 2.6 Genome Variations and Their Consequences; 2.7 Genomics; 2.8 The Role of Genomics in Pharmaceutical Research and Clinical Practice; 2.9 Proteins; 2.10 Bioinformatics; Supplementary Reading; Chapter 3 Microarrays; 3.1 Types of Microarray Experiments; 3.1.1 Experiment Type 1: Tissue-Specific Gene Expression; 3.1.2 Experiment Type 2: Developmental Genetics; 3.1.3 Experiment Type 3: Genetic Diseases; 3.1.4 Experiment Type 4: Complex Diseases 3.1.5 Experiment Type 5: Pharmacological Agents3.1.6 Experiment Type 6: Plant Breeding; 3.1.7 Experiment Type 7: Environmental Monitoring; 3.2 A Very Simple Hypothetical Microarray Experiment; 3.3 A Typical Microarray Experiment; 3.3.1 Microarray Preparation; 3.3.2 Sample Preparation; 3.3.3 The Hybridization Step; 3.3.4 Scanning the Microarray; 3.3.5 Interpreting the Scanned Image; 3.4 Multichannel cDNA Microarrays; 3.5 Oligonucleotide Microarrays; 3.6 Bead-Based Arrays; 3.7 Confirmation of Microarray Results; Supplementary Reading and Electronic References Chapter 4 Processing the Scanned Image4.1 Converting the Scanned Image to the Spotted Image; 4.1.1 Gridding; 4.1.2 Segmentation; 4.1.3 Quantification; 4.2 Quality Assessment; 4.2.1 Visualizing the Spotted Image; 4.2.2 Numerical Evaluation of Array Quality; 4.2.3 Spatial Problems; 4.2.4 Spatial Randomness; 4.2.5 Quality Control of Arrays; 4.2.6 Assessment of Spot Quality; 4.3 Adjusting for Background; 4.3.1 Estimating the Background; 4.3.2 Adjusting for the Estimated Background; 4.4 Expression-Level Calculation for Two-Channel cDNA Microarrays 4.5 Expression-Level Calculation for Oligonucleotide Microarrays4.5.1 The Average Difference; 4.5.2 A Weighted Average Difference; 4.5.3 Perfect Matches Only; 4.5.4 Background Adjustment Approach; 4.5.5 Model-Based Approach; 4.5.6 Absent-Present Calls; Supplementary Reading; Software Notes; Chapter 5 Preprocessing Microarray Data; 5.1 Logarithmic Transformation; 5.2 Variance Stabilizing Transformations; 5.3 Sources of Bias; 5.4 Normalization; 5.5 Intensity-Dependent Normalization; 5.5.1 Smooth Function Normalization; 5.5.2 Quantile Normalization; 5.5.3 Stagewise Normalization 5.5.4 Normalization of Two-Channel Arrays |
| Record Nr. | UNINA-9910138960903321 |
Amaratunga Dhammika <1956->
|
||
| Hoboken, New Jersey : , : John Wiley & Sons, , 2014 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Exploration and analysis of DNA microarray and other high dimensional data / / Dhammika Amaratunga, Javier Cabrera, Ziv Shkedy, authors
| Exploration and analysis of DNA microarray and other high dimensional data / / Dhammika Amaratunga, Javier Cabrera, Ziv Shkedy, authors |
| Autore | Amaratunga Dhammika <1956-> |
| Edizione | [Second edition.] |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, , 2014 |
| Descrizione fisica | 1 online resource (346 p.) |
| Disciplina | 572/.636 |
| Altri autori (Persone) |
CabreraJavier
ShkedyZiv |
| Collana | Wiley series in probability and statistics |
| Soggetto topico | Protein microarrays - Statistical methods |
| ISBN |
1-118-36450-3
1-118-36453-8 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Contents; Preface; Chapter 1 A Brief Introduction; 1.1 A Note on Exploratory Data Analysis; 1.2 Computing Considerations and Software; 1.3 A Brief Outline of the Book; 1.4 Data Sets and Case Studies; 1.4.1 The Golub Data; 1.4.2 The Mouse5 Data; 1.4.3 The Khan Data; 1.4.4 The Sialin Data; 1.4.5 The Behavioral Study Data; 1.4.6 The Spiked-In Data; 1.4.7 The APOAI Study; 1.4.8 The Breast Cancer Data; 1.4.9 Platinum Spike Data Set; 1.4.10 Human Epidermal Squamous Carcinoma Cell Line A431 Experiment; 1.4.11 Note: Public Repositories of Microarray Data; Chapter 2 Genomics Basics
2.1 Genes2.2 Deoxyribonucleic Acid; 2.3 Gene Expression; 2.4 Hybridization Assays and Other Laboratory Techniques; 2.5 The Human Genome; 2.6 Genome Variations and Their Consequences; 2.7 Genomics; 2.8 The Role of Genomics in Pharmaceutical Research and Clinical Practice; 2.9 Proteins; 2.10 Bioinformatics; Supplementary Reading; Chapter 3 Microarrays; 3.1 Types of Microarray Experiments; 3.1.1 Experiment Type 1: Tissue-Specific Gene Expression; 3.1.2 Experiment Type 2: Developmental Genetics; 3.1.3 Experiment Type 3: Genetic Diseases; 3.1.4 Experiment Type 4: Complex Diseases 3.1.5 Experiment Type 5: Pharmacological Agents3.1.6 Experiment Type 6: Plant Breeding; 3.1.7 Experiment Type 7: Environmental Monitoring; 3.2 A Very Simple Hypothetical Microarray Experiment; 3.3 A Typical Microarray Experiment; 3.3.1 Microarray Preparation; 3.3.2 Sample Preparation; 3.3.3 The Hybridization Step; 3.3.4 Scanning the Microarray; 3.3.5 Interpreting the Scanned Image; 3.4 Multichannel cDNA Microarrays; 3.5 Oligonucleotide Microarrays; 3.6 Bead-Based Arrays; 3.7 Confirmation of Microarray Results; Supplementary Reading and Electronic References Chapter 4 Processing the Scanned Image4.1 Converting the Scanned Image to the Spotted Image; 4.1.1 Gridding; 4.1.2 Segmentation; 4.1.3 Quantification; 4.2 Quality Assessment; 4.2.1 Visualizing the Spotted Image; 4.2.2 Numerical Evaluation of Array Quality; 4.2.3 Spatial Problems; 4.2.4 Spatial Randomness; 4.2.5 Quality Control of Arrays; 4.2.6 Assessment of Spot Quality; 4.3 Adjusting for Background; 4.3.1 Estimating the Background; 4.3.2 Adjusting for the Estimated Background; 4.4 Expression-Level Calculation for Two-Channel cDNA Microarrays 4.5 Expression-Level Calculation for Oligonucleotide Microarrays4.5.1 The Average Difference; 4.5.2 A Weighted Average Difference; 4.5.3 Perfect Matches Only; 4.5.4 Background Adjustment Approach; 4.5.5 Model-Based Approach; 4.5.6 Absent-Present Calls; Supplementary Reading; Software Notes; Chapter 5 Preprocessing Microarray Data; 5.1 Logarithmic Transformation; 5.2 Variance Stabilizing Transformations; 5.3 Sources of Bias; 5.4 Normalization; 5.5 Intensity-Dependent Normalization; 5.5.1 Smooth Function Normalization; 5.5.2 Quantile Normalization; 5.5.3 Stagewise Normalization 5.5.4 Normalization of Two-Channel Arrays |
| Record Nr. | UNINA-9910810663903321 |
|
Amaratunga Dhammika <1956->
|
||
| Hoboken, New Jersey : , : John Wiley & Sons, , 2014 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Exploration and analysis of DNA microarray and protein array data [[electronic resource] /] / Dhammika Amaratunga, Javier Cabrera
| Exploration and analysis of DNA microarray and protein array data [[electronic resource] /] / Dhammika Amaratunga, Javier Cabrera |
| Autore | Amaratunga Dhammika <1956-> |
| Pubbl/distr/stampa | Hoboken, NJ, : John Wiley, c2004 |
| Descrizione fisica | 1 online resource (270 p.) |
| Disciplina |
572.8
572.8636 |
| Altri autori (Persone) | CabreraJavier |
| Collana | Wiley series in probability and statistics |
| Soggetto topico |
DNA microarrays - Statistical methods
Protein microarrays - Statistical methods |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-282-30744-4
9786612307447 0-470-31712-4 0-470-31796-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Exploration and Analysis of DNA Microarray and Protein A rray Data; Contents; Preface; 1. A Brief Introduction; 1.1. A Note on Exploratory Data Analysis; 1.2. Computing Considerations and Software; 1.3. A Brief Outline of the Book; 2. Genomics Basics; 2.1. Genes; 2.2. DNA; 2.3. Gene Expression; 2.4. Hybridization Assays and Other Laboratory Techniques; 2.5. The Human Genome; 2.6. Genome Variations and Their Consequences; 2.7. Genomics; 2.8. The Role of Genomics in Pharmaceutical Research; 2.9. Proteins; 2.10. Bioinformatics; Supplementary Reading; Exercises; 3. Microarrays
3.1. Types of Microarray Experiments3.1.1. Experiment Type 1: Tissue-Specific Gene Expression; 3.1.2. Experiment Type 2: Developmental Genetics; 3.1.3. Experiment Type 3: Genetic Diseases; 3.1.4. Experiment Type 4: Complex Diseases; 3.1.5. Experiment Type 5: Pharmacological Agents; 3.1.6. Experiment Type 6: Plant Breeding; 3.1.7. Experiment Type 7: Environmental Monitoring; 3.2. A Very Simple Hypothetical Microarray Experiment; 3.3. A Typical Microarray Experiment; 3.3.1. Microarray Preparation; 3.3.2. Sample Preparation; 3.3.3. The Hybridization Step; 3.3.4. Scanning the Microarray 3.3.5. Interpreting the Scanned Image3.4. Multichannel cDNA Microarrays; 3.5. Oligonucleotide Arrays; 3.6. Bead-Based Arrays; 3.7. Confirmation of Microarray Results; Supplementary Reading and Electronic References; Exercises; 4. Processing the Scanned Image; 4.1. Converting the Scanned Image to the Spotted Image; 4.1.1. Gridding; 4.1.2. Segmentation; 4.1.3. Quantification; 4.2. Quality Assessment; 4.2.1. Visualizing the Spotted Image; 4.2.2. Numerical Evaluation of Array Quality; 4.2.3. Spatial Problems; 4.2.4. Spatial Randomness; 4.2.5. Quality Control of Arrays 4.2.6. Assessment of Spot Quality4.3. Adjusting for Background; 4.3.1. Estimating the Background; 4.3.2. Adjusting for the Estimated Background; 4.4. Expression Level Calculation for Two-Channel cDNA Microarrays; 4.5. Expression Level Calculation for Oligonucleotide Arrays; 4.5.1. The Average Difference; 4.5.2. A Weighted Average Difference; 4.5.3. Perfect Matches Only; 4.5.4. Background Adjustment Approach; 4.5.5. Model-Based Approach; 4.5.6. Absent-Present Calls; Supplementary Reading; Exercises; 5. Preprocessing Microarray Data; 5.1. Logarithmic Transformation 5.2. Variance Stabilizing Transformations5.3. Sources of Bias; 5.4. Normalization; 5.5. Intensity-Dependent Normalization; 5.5.1. Smooth Function Normalization; 5.5.2. Quantile Normalization; 5.5.3. Normalization of Oligonucleotide Arrays; 5.5.4. Normalization of Two-Channel Arrays; 5.5.5. Spatial Normalization; 5.5.6. Stagewise Normalization; 5.6. Judging the Success of a Normalization; 5.7. Outlier Identification; 5.7.1 Nonresistant Rules for Outlier Identification; 5.7.2. Resistant Rules for Outlier Identification; 5.8. Assessing Replicate Array Quality; Exercises; 6. Summarization 6.1. Replication |
| Record Nr. | UNINA-9910144683203321 |
|
Amaratunga Dhammika <1956->
|
||
| Hoboken, NJ, : John Wiley, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Exploration and analysis of DNA microarray and protein array data [[electronic resource] /] / Dhammika Amaratunga, Javier Cabrera
| Exploration and analysis of DNA microarray and protein array data [[electronic resource] /] / Dhammika Amaratunga, Javier Cabrera |
| Autore | Amaratunga Dhammika <1956-> |
| Pubbl/distr/stampa | Hoboken, NJ, : John Wiley, c2004 |
| Descrizione fisica | 1 online resource (270 p.) |
| Disciplina |
572.8
572.8636 |
| Altri autori (Persone) | CabreraJavier |
| Collana | Wiley series in probability and statistics |
| Soggetto topico |
DNA microarrays - Statistical methods
Protein microarrays - Statistical methods |
| ISBN |
1-282-30744-4
9786612307447 0-470-31712-4 0-470-31796-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Exploration and Analysis of DNA Microarray and Protein A rray Data; Contents; Preface; 1. A Brief Introduction; 1.1. A Note on Exploratory Data Analysis; 1.2. Computing Considerations and Software; 1.3. A Brief Outline of the Book; 2. Genomics Basics; 2.1. Genes; 2.2. DNA; 2.3. Gene Expression; 2.4. Hybridization Assays and Other Laboratory Techniques; 2.5. The Human Genome; 2.6. Genome Variations and Their Consequences; 2.7. Genomics; 2.8. The Role of Genomics in Pharmaceutical Research; 2.9. Proteins; 2.10. Bioinformatics; Supplementary Reading; Exercises; 3. Microarrays
3.1. Types of Microarray Experiments3.1.1. Experiment Type 1: Tissue-Specific Gene Expression; 3.1.2. Experiment Type 2: Developmental Genetics; 3.1.3. Experiment Type 3: Genetic Diseases; 3.1.4. Experiment Type 4: Complex Diseases; 3.1.5. Experiment Type 5: Pharmacological Agents; 3.1.6. Experiment Type 6: Plant Breeding; 3.1.7. Experiment Type 7: Environmental Monitoring; 3.2. A Very Simple Hypothetical Microarray Experiment; 3.3. A Typical Microarray Experiment; 3.3.1. Microarray Preparation; 3.3.2. Sample Preparation; 3.3.3. The Hybridization Step; 3.3.4. Scanning the Microarray 3.3.5. Interpreting the Scanned Image3.4. Multichannel cDNA Microarrays; 3.5. Oligonucleotide Arrays; 3.6. Bead-Based Arrays; 3.7. Confirmation of Microarray Results; Supplementary Reading and Electronic References; Exercises; 4. Processing the Scanned Image; 4.1. Converting the Scanned Image to the Spotted Image; 4.1.1. Gridding; 4.1.2. Segmentation; 4.1.3. Quantification; 4.2. Quality Assessment; 4.2.1. Visualizing the Spotted Image; 4.2.2. Numerical Evaluation of Array Quality; 4.2.3. Spatial Problems; 4.2.4. Spatial Randomness; 4.2.5. Quality Control of Arrays 4.2.6. Assessment of Spot Quality4.3. Adjusting for Background; 4.3.1. Estimating the Background; 4.3.2. Adjusting for the Estimated Background; 4.4. Expression Level Calculation for Two-Channel cDNA Microarrays; 4.5. Expression Level Calculation for Oligonucleotide Arrays; 4.5.1. The Average Difference; 4.5.2. A Weighted Average Difference; 4.5.3. Perfect Matches Only; 4.5.4. Background Adjustment Approach; 4.5.5. Model-Based Approach; 4.5.6. Absent-Present Calls; Supplementary Reading; Exercises; 5. Preprocessing Microarray Data; 5.1. Logarithmic Transformation 5.2. Variance Stabilizing Transformations5.3. Sources of Bias; 5.4. Normalization; 5.5. Intensity-Dependent Normalization; 5.5.1. Smooth Function Normalization; 5.5.2. Quantile Normalization; 5.5.3. Normalization of Oligonucleotide Arrays; 5.5.4. Normalization of Two-Channel Arrays; 5.5.5. Spatial Normalization; 5.5.6. Stagewise Normalization; 5.6. Judging the Success of a Normalization; 5.7. Outlier Identification; 5.7.1 Nonresistant Rules for Outlier Identification; 5.7.2. Resistant Rules for Outlier Identification; 5.8. Assessing Replicate Array Quality; Exercises; 6. Summarization 6.1. Replication |
| Record Nr. | UNINA-9910829878103321 |
|
Amaratunga Dhammika <1956->
|
||
| Hoboken, NJ, : John Wiley, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Exploration and analysis of DNA microarray and protein array data [[electronic resource] /] / Dhammika Amaratunga, Javier Cabrera
| Exploration and analysis of DNA microarray and protein array data [[electronic resource] /] / Dhammika Amaratunga, Javier Cabrera |
| Autore | Amaratunga Dhammika <1956-> |
| Pubbl/distr/stampa | Hoboken, NJ, : John Wiley, c2004 |
| Descrizione fisica | 1 online resource (270 p.) |
| Disciplina |
572.8
572.8636 |
| Altri autori (Persone) | CabreraJavier |
| Collana | Wiley series in probability and statistics |
| Soggetto topico |
DNA microarrays - Statistical methods
Protein microarrays - Statistical methods |
| ISBN |
1-282-30744-4
9786612307447 0-470-31712-4 0-470-31796-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Exploration and Analysis of DNA Microarray and Protein A rray Data; Contents; Preface; 1. A Brief Introduction; 1.1. A Note on Exploratory Data Analysis; 1.2. Computing Considerations and Software; 1.3. A Brief Outline of the Book; 2. Genomics Basics; 2.1. Genes; 2.2. DNA; 2.3. Gene Expression; 2.4. Hybridization Assays and Other Laboratory Techniques; 2.5. The Human Genome; 2.6. Genome Variations and Their Consequences; 2.7. Genomics; 2.8. The Role of Genomics in Pharmaceutical Research; 2.9. Proteins; 2.10. Bioinformatics; Supplementary Reading; Exercises; 3. Microarrays
3.1. Types of Microarray Experiments3.1.1. Experiment Type 1: Tissue-Specific Gene Expression; 3.1.2. Experiment Type 2: Developmental Genetics; 3.1.3. Experiment Type 3: Genetic Diseases; 3.1.4. Experiment Type 4: Complex Diseases; 3.1.5. Experiment Type 5: Pharmacological Agents; 3.1.6. Experiment Type 6: Plant Breeding; 3.1.7. Experiment Type 7: Environmental Monitoring; 3.2. A Very Simple Hypothetical Microarray Experiment; 3.3. A Typical Microarray Experiment; 3.3.1. Microarray Preparation; 3.3.2. Sample Preparation; 3.3.3. The Hybridization Step; 3.3.4. Scanning the Microarray 3.3.5. Interpreting the Scanned Image3.4. Multichannel cDNA Microarrays; 3.5. Oligonucleotide Arrays; 3.6. Bead-Based Arrays; 3.7. Confirmation of Microarray Results; Supplementary Reading and Electronic References; Exercises; 4. Processing the Scanned Image; 4.1. Converting the Scanned Image to the Spotted Image; 4.1.1. Gridding; 4.1.2. Segmentation; 4.1.3. Quantification; 4.2. Quality Assessment; 4.2.1. Visualizing the Spotted Image; 4.2.2. Numerical Evaluation of Array Quality; 4.2.3. Spatial Problems; 4.2.4. Spatial Randomness; 4.2.5. Quality Control of Arrays 4.2.6. Assessment of Spot Quality4.3. Adjusting for Background; 4.3.1. Estimating the Background; 4.3.2. Adjusting for the Estimated Background; 4.4. Expression Level Calculation for Two-Channel cDNA Microarrays; 4.5. Expression Level Calculation for Oligonucleotide Arrays; 4.5.1. The Average Difference; 4.5.2. A Weighted Average Difference; 4.5.3. Perfect Matches Only; 4.5.4. Background Adjustment Approach; 4.5.5. Model-Based Approach; 4.5.6. Absent-Present Calls; Supplementary Reading; Exercises; 5. Preprocessing Microarray Data; 5.1. Logarithmic Transformation 5.2. Variance Stabilizing Transformations5.3. Sources of Bias; 5.4. Normalization; 5.5. Intensity-Dependent Normalization; 5.5.1. Smooth Function Normalization; 5.5.2. Quantile Normalization; 5.5.3. Normalization of Oligonucleotide Arrays; 5.5.4. Normalization of Two-Channel Arrays; 5.5.5. Spatial Normalization; 5.5.6. Stagewise Normalization; 5.6. Judging the Success of a Normalization; 5.7. Outlier Identification; 5.7.1 Nonresistant Rules for Outlier Identification; 5.7.2. Resistant Rules for Outlier Identification; 5.8. Assessing Replicate Array Quality; Exercises; 6. Summarization 6.1. Replication |
| Record Nr. | UNINA-9910840592303321 |
|
Amaratunga Dhammika <1956->
|
||
| Hoboken, NJ, : John Wiley, c2004 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||